300 Protein features that represent the mapping between Ensembl proteins (ENSP) and AlphaFoldDB protein structures (including their corresponding chains). Imported via UniProt mappings AFDB-ENSP mappings 1 \N 276 Conserved Domain Database models. CDD 1 {"type": "domain"} 47 Covariance models from Rfam (release 12.2), aligned to the genome with 'cmscan' from the Infernal suite of programs. Models are restricted to those observed in species that share a last common ancestor (LCA). Rfam Models (LCA) 1 {"type": "rna"} 27 Density of coding genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.) Coding genes (density) 1 \N 39 Dust is a program that identifies low-complexity sequences (regions of the genome with a biased distribution of nucleotides, such as a repeat). The Dust module is widely used with BLAST to prevent 'sticky' regions from determining false hits. Low complexity (Dust) 1 \N 1 Protein coding genes annotated in ENA Genes 1 {"label_key": "[biotype]", "caption": "Genes", "colour_key": "[biotype]", "default": {"cytoview": "gene_label", "MultiBottom": "collapsed_label", "alignsliceviewbottom": "as_collapsed_label", "MultiTop": "gene_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label"}, "name": "Genes", "key": "ensembl"} 18 Assembly gap feature annotated in ENA Assembly gap (ENA) 1 \N 17 mRNA feature annotated in ENA mRNA (ENA) 1 {"caption": "Genomic features", "key": "ena_features", "label_key": "[text_label] [display_label]", "multi_name": "Genomic features", "name": "Genomic features"} 295 CATH/Gene3D families. Gene3D 1 {"type": "domain"} 2 Cross-references attached by GenomeLoader GenomeLoader cross-references 0 \N 302 \N GOA annotation 0 \N 55 GO term derived transitively from a UniProt record UniProt-derived GO term 0 \N 62 Gene encoding an enzyme annotated at the Plant Reactome. Plant Reactome 1 \N 277 HAMAP families. HAMAP 1 {"type": "domain"} 280 PANTHER families. PANTHER 1 {"type": "domain"} 298 InterPro2GO mapping, defined by InterPro. InterPro2GO mapping 0 \N 44 Density of long non-coding RNA genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.) Long non-coding genes (density) 1 \N 49 MicroRNA from miRBase. miRBase miRNA 1 {"type": "rna"} 290 Intrinsically disordered regions predicted by MobiDB lite. MobiDB lite 1 {"type": "feature"} 291 Coiled-coil regions predicted by Ncoils. Coiled-coils (Ncoils) 1 {"type": "feature"} 46 Percentage of repetitive elements for top level sequences (such as chromosomes, scaffolds, etc.) Repeats (percent) 1 \N 19 Percentage of G/C bases in the sequence. GC content 1 \N 278 Protein domains and motifs from the Pfam database. Pfam 1 {"type": "domain"} 296 Protein domains and motifs from the PROSITE profiles database. PROSITE profiles 1 {"type": "domain"} 281 Protein domains and motifs from the PIR (Protein Information Resource) Superfamily database. PIRSF 1 {"type": "domain"} 282 Protein fingerprints (groups of conserved motifs) from the PRINTS database. Prints 1 {"type": "domain"} 45 Density of pseudogenes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.) Pseudogenes (density) 1 \N 42 Repeats detected using the MIPS Repeat Database (REdat) using RepeatMasker. Repeats: REdat 1 \N 40 Repeats identified by RepeatMasker, using the Repbase library of repeat profiles. Repeats: Repbase 1 \N 52 RNA genes produced by filtering alignments of Rfam (release 12.2) covariance models. RNA genes 1 {"label_key": "[biotype]", "caption": "Genes", "colour_key": "[biotype]", "default": {"cytoview": "gene_label", "MultiBottom": "collapsed_label", "alignsliceviewbottom": "as_collapsed_label", "MultiTop": "gene_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label"}, "name": "Genes", "key": "ensembl"} 297 Protein domains and motifs from the PROSITE patterns database. PROSITE patterns 1 {"type": "domain"} 289 Low complexity peptide sequences identified by Seg. Low complexity (Seg) 1 {"type": "feature"} 285 Structure-Function Linkage Database families. SFLD 1 {"type": "domain"} 43 Density of short non-coding RNA genes, calculated by dividing the chromosome into 150 "bins" and counting the genes in each. (For very short chromosomes, e.g. MT, some genes contribute to multiple bins.) Short non-coding genes (density) 1 \N 288 Signal peptide cleavage sites predicted by SignalP. Cleavage site (Signalp) 1 {"type": "feature"} 284 Protein domains and motifs from the SMART database. SMART 1 {"type": "domain"} 287 Protein domains and motifs from the SUPERFAMILY database. Superfamily 1 {"type": "domain"} 286 Protein domains and motifs from the TIGRFAM database. TIGRFAM 1 {"type": "domain"} 292 Transmembrane helices predicted by TMHMM. Transmembrane helices 1 {"type": "feature"} 41 Tandem Repeats Finder locates adjacent copies of a pattern of nucleotides. Tandem repeats (TRF) 1 \N 48 tRNA models predicted with tRNAscan-SE (release 1.3.1). tRNA Models 1 {"type": "rna"} 51 RNA genes produced by filtering predictions from tRNAscan-SE v1.23. RNA genes 1 {"label_key": "[biotype]", "caption": "Genes", "colour_key": "[biotype]", "default": {"cytoview": "gene_label", "MultiBottom": "collapsed_label", "alignsliceviewbottom": "as_collapsed_label", "MultiTop": "gene_label", "contigviewbottom": "transcript_label", "contigviewtop": "gene_label"}, "name": "Genes", "key": "ensembl"} 53 UniParc mapping based on sequence checksums UniParc cross-reference 0 \N 54 UniProt cross-reference derived transitively from a UniParc identifier UniParc-derived cross-reference 0 \N 56 Cross-reference derived transitively from a UniProt record UniProt-derived cross-reference 0 \N 59 Cross references to RefSeq nucleotide sequences, determined by alignment against the transcriptome with blastx. RefSeq transcripts 0 \N 58 Cross references to RefSeq peptide sequences, determined by alignment against the proteome with blastp. RefSeq peptides 0 \N 57 Cross references to UniProt Swiss-Prot (reviewed) proteins, determined by alignment against the proteome with blastp. UniProt reviewed proteins 0 \N 60 Cross references to UniProt TrEMBL (unreviewed) proteins, determined by alignment against the proteome with blastp. UniProt unreviewed proteins 0 \N